The Reign of Captain Swan
by alexandra142
Summary: Storybrooke has been destroyed and everyone is back in their homes. Emma and Killian are the dark ones, and Snow and David are the queen and king. Emma and Killian are wreaking havoc and fear throughout the land. What will happen?
1. Chapter 1

Storybrooke was destroyed and everybody was sent back to the Enchanted forest. Snow and Charming were queen and king, and the citizens were all happy. The enchanted kingdom was all restored and nothing was ruble like it used to be. It was back to normal, but the villains were now Emma Swan and Killian Jones. The two of them tortured villages and spread fear throughout the land. Regina refurbished her old home and lived in it with Henry.

Snow and Charming worked hard to keep peace and regrow the prosperity the kingdom used to have. Nothing was coming easy and the fear of the people made it even harder. One day while Snow was playing with Neal she said, "Are we good parents, David?"

"Of course we are. You of all people should know that," David said reassuring Snow.

"Why does our own daughter terrorize our kingdom?" Snow said terrified as she looked outside.

"It's not her Snow. It's the dark one not Emma."

"Emma and Killian have a choice. It's not just the dark one. There is always a choice David."

They had given up on vanquishing the darkness. Almost everybody had lost hope for Emma and Killian except for Regina and Henry. Killian and Emma had a trip to the Underworld, but they came out alive evil as ever. Henry and Regina tried everything to keep Operation Light Swan, now Operation Light Captain Swan, to succeed. They tried talking to Emma and Killian, but they were stuck in the darkness. They tried kidnapping the two of them, but the two of them would always escape. The savior was the most feared sorceress, and Killian the most feared sorcerer. They were feared more than any villain, more than the Evil Queen was feared.

"I never should've given up on Emma," Charming said.

"But you did," Emma said in a monotonous voice appearing.

"What are you doing here?" Snow said as she held Neal closer.

"I just came to visit my baby brother," Emma said as she caressed her brother's cheek.

"What do you want dark one?" Charming said as he placed a hand on his sword.

"I thought you were regretting giving up on me. So tell me the truth have you missed Killian and I?" Emma mocked.

"Of course we missed you, we missed the real you and Killian," Snow said.

"That's why I have given up on you. You see, mom, this is who I am and who Killian is," Emma said annoyed.

"No it isn't, but if you've just come to remind us of our mistakes please leave," David said.

"Don't worry about me, but I'll be back, and don't ever speak my name unless you'd like to summon me," Emma said as she disappeared.

* * *

"Hello love," Killian said as he placed his hand and hook on Emma's arms.

They were in Rumpelstiltskin's home, they kicked the old crocodile out and him and Belle lived in a village near Regina. The castle was now modern and it was based off of everything in Emma's old home at Storybrooke and Killian's Jolly Roger. They renovated the dungeon with unbreakable glass walls that were immune to all magic except dark one magic. The castle had more large glass windows that were tinted black on the outside. The whole castle was based on dark hues, from black to gray to dark blue. The castle could always be renovated with magic, and it was renovated whenever Killian or Emma felt it need an renovated. Emma and Killian each had a room and they designed and changed it as much as they wanted.

Emma pulled herself closer to Killian, and smiled. "It feels like I haven't seen you for years. I missed you," Emma said.

"Aye, me too. I can't believe you were only gone for a week, but it felt like years, but then again we don't feel time like others," Killian said as he laughed.

Killian placed his soft lips onto Emma's. They kissed, their lips moved in perfect unison. They were made for each other in light and darkness. They finally pulled themselves away from each other. "How was your trip love?" Killian asked.

"It was fine," Emma said as she pulled out a seat from the dining table and sat down.

"How's Henry?"

"He's fine, but he still doesn't understand."

"Did you invite him over here?"

"Yes, but he refused to come over until I became the 'real' me."

* * *

 **Thank you for reading, please leave a review if you'd like me to continue! _lm1212_**


	2. Chapter 2

Henry trained every day, he'd wake up at the break of dawn, and sleep late. In the morning he'd hang out with knights and would improve his sword fighting skills. Henry was beginning to be one of the best knights in all the realm, but all he wished for was that his mother, Emma, would be proud of him. Henry wanted to follow in his grandfathers footsteps, slay a dragon, take care of the kingdom, and become a hero. Regina was always be proud of him, but he wished Emma or even Killian would support him.

It was already lunch time and Henry decided to stop by the castle to visit his other mom, Regina. Henry, Regina, Robin, his son, his daughter, and Zelena lived in the castle. Zelena was more of prisoner, but she was free to spend time with her daughter, although Regina made sure the bracelet was on Zelena at all times. Regina and Robin Hood took care of a small kingdom of their own, but it wasn't as large as Snow and Charming's. Emma would visit them time to time to talk with Henry, but those visits were cut short because they ended up in an argument. Regina couldn't help to feel pained for Henry and Emma, because Regina knew how important it was to have a bond with your mother. Regina couldn't help but worry that Henry might go on the same dark path she'd went on. When Regina saw Henry she said, "Hey, how are you doing?"

"Hey mom, I'm doing fine," Henry replied as ate his lunch.

"Are you sure? It seems you're more worried than ever since your mom's last visit."

"Yeah, what if she never gets better? I don't want to lose her forever. I don't want to be the kid who everybody is afraid of because one of his mom's was the evil queen and the other a dark one."

"Hey don't think like that. You and I know very well Emma will get out of this as a hero, Killian as well."

"I guess."

"Rumpelstiltskin came out as a hero after centuries of darkness. If the old crocodile could do it anybody else can."

"How is Rumpel doing?"

"He's living his happy ending with Belle. Hopefully the pirate never finds Rumpelstiltskin because if Killian does we both know what'll happen."

"I'm gonna go back to the knights," Henry said as he finished his lunch.

"Be safe.'

"See you tonight."

"I'll see you tonight," Regina said as she hugged Henry.

Henry left the room. Robin Hood rushed in and was out of breath he said, "K-Killian and Emma they were here. They took Zelena."

"Damn it, seriously? This is Storybrooke deja vu with two dark ones," Regina said annoyed.

"We've to get Zelena back. Who knows what the dark ones will do?"

"No, you've got to stay here and take care of the place. I'm going to go to their castle," Regina said and disappeared before Robin could say anything.

* * *

"I knew you two could never help yourselves," Zelena said.

"It's good to see you too, Wicked Witch," Killian said as he toyed with his hook. He could have a real hand if he wanted, but Killian enjoyed killing victims with his Hook much more than he did with his hand.

"What do you want?" Zelena asked.

"We're here to offer you a deal," Emma said.

"Spoken like a true dark one," Zelena said.

"Tell us everything you know about Rumpel, ally with us, and you'll have protection from us and your magic back," Killian said as he pointed at Zelena's black bracelet.

"This sounds like a deal I failed to make with Emma back in Storybrooke," Zelena said.

"Will you take it or not? We are happy to bring you back to Regina, and you could stay as a prisoner, or you could make this deal. It's your choice mate, so make the right one," Killian threatened.

"If that's what makes you happy dearies," Zelena said.

Emma waved her hand and the bracelet on Zelena's wrist fell off. "Rumpel and Belle live in a village in Regina's kingdom. I can lead you there as long as I get to have fun as well," Regina slyly said.

"KILLIAN! EMMA!" Regina yelled.

"Ugh, sister you don't need to be so loud," Zelena said.

"What do you need with Zelena?" Regina said as she threw a fireball at Zelena.

"Ooooo sis, your such a failure," Zelena said as she reflected the fireball back at Regina.

Regina flew backwards and slammed against a wall. Emma grabbed the black and leather bracelet that used to be on Zelena and placed it onto Regina's wrist. "Lovely, I'll put her in the dungeon," Killian said as he disappeared with Regina.

* * *

 **Thank you for reading, please leave a review if you'd like me to continue! _lm1212_**


	3. Chapter 3

Robin sat in the dining room where Regina left him, he waited and waited for Regina to return. We waited for hours until he heard somebody walked in, Robin immediately stood up to look at who it was.

"Robin?" Henry questioned as he entered.

"Oh-, Henry," Robin said disappointed.

"Wh-what's wrong? Do you know where mom is?" Henry asked.

"I don't know, she went to the dark one residence, and never came back. The dark ones took Zelena, and Regina went after them. I'm worried for her Henry," Robin said.

"Wait, mom, I mean, Emma, was here?"

"Yes, but I couldn't stop her."

"We have to go to the Dark One castle, and save Regina."

"Yes, we should bring a couple knights with us, we should be able to make it there in a few days."

Robin and Henry gathered up some basic supplies, and then rounded up a few knights. Each person road a beautiful and well-taken care of horse. They started their journey into the

* * *

"Hello sister," Zelena said excited.

Regina looked around. She was trapped in a room made of glass, arms were bound, and Zelena was outside of the glass room. Emma and Killian stood to the side as they watched Zelena. Regina tried to move her hands to use magic to unbind herself, but it didn't work. She tried a couple of times, but it didn't work. She looked up confused.

"Love, your magic isn't going to work in that room. No matter how hard you try," Killian said amused.

Regina missed the days where she could joke about Killian's guy liner, and have a _"_ _savior"_ believe in her. Those days were long gone, and they would be as gone as Storybrooke was.

"What do you want?" Regina said as she gritted her teeth.

"To break your heart, have your life, to find love," Zelena started as she was slowing turning green.

"Your cooperation, and to do that we'll need your heart," Emma said cutting Zelena off and appeared right next to Regina in the glass room.

Regina looked petrified. Regina was tied to a chair, and her face was inches away from Emma's. Regina thought, " _hopefully the protection spell I put on my heart will do me some good right now."_ Emma plunged her hand into Regina's chest, and Regina violently jerked back into the chair. Emma pulled her hand out, and it was a beating red slightly tainted heart. Emma exited the room and then magically unbounded Regina. Regina immediately tried to escape the room, but it didn't work. Emma handed Killian, Regina's heart like it was a toy.

"Love didn't I already tell you, you can't escape that room with magic," Killian said as he held Regina's heart in his hand.

"Sister, unfortunately these two won't let me kill you, but soon I'll be able to do whatever I want to you," Zelena snickered.

Killian waved his hand over Regina's heart and then tossed it to Zelena. "Do whatever you'd like Zelena, but Killian just placed a spell so that if you try to kill Regina it will not work. The heart will be given to one of us," Emma said as she and Killian started walking out.

"You'll never get away with this Emma. Killian and you may be the dark ones, but we have an army," Regina retaliated.

"Oh, shut up, sis," Zelena said as she held Regina's heart.

"Who's the we your talking about? Your mistaken about one thing love, Emma and I do have an army," Killian chuckled.

* * *

"I just got word that the dark ones arrived at Regina's castle and took Zelena, and Regina went to the Dark One Castle. The men at Regina's castle haven't seen her arrive back," A knight said.

"Thank you," Snow said.

The knight walked out the room. A crib was to the side of the room and a unicorn mobile, that was once for Emma, hung from the ceiling. David was off training with the knights, while Snow took care of baby Neal. Snow leaned against a wall and held baby Neal close to contemplate. Snow was hopeless, she wished she could help her daughter. As much as Henry tried it never worked. Maybe it was time to capture the dark ones, like her and David had done to Rumpelstiltskin. Emma was Snow's daughter, but what if it would help the greater good, would it be okay? Snow tried to shake off the thought of capturing Killian and Emma.

"I love you," Snow said as she tickled Neal's cheek.

* * *

 **Thank you for reading! Please leave a review to tell me to continue or give me any suggestions. _lm1212_**


	4. Chapter 4

"Belle, dear?" Rumpelstiltskin called out.

It was a warm sunny day, the birds were chirping, and the people in town were happy. Rumpelstiltskin was no longer feared, but he was still hated by some.

"I'm outside Rumpel!" Belle called back.

Belle sat outside on a stump and was spotlighted by a beam of sun. She wore a blue dress and brown boots. Her beautiful brown curls reflected the sun in the perfect ways. She gazed at the wild and admired it.

"I was just admiring the beauty of this day," Belle said happily.

"The only beauty I see is sitting right here," Rumpel replied.

"Aw, thanks Rumpel. What's up?"

"I fear it's the worst. The dark ones have taken Zelena, one of the knights from Regina's castle just came here to warn us."

"Do we have to leave?"

"I fear so."

"Rumpel, you can't be the coward you were. You must face your fears like you did in Storybrooke, when you fought the bear to save me. You need to find that courage again. We can't keep running every time you suspect Ki-Hook might know where we are."

"Yes, but Merida was a person who had emotions. Hook, he's just out for revenge."

"Fine, we can run, but this has to be the last time."

"Thank you Belle, let's pack our stuff."

* * *

"No, we should attack from here." Grumpy argued.

A team was assembled around a wooden circle table. Figurines and a Dark One Castle figurine laid on the table. Charming had made the decision that it was time Killian and Emma were captured. All he could think was " _Am I being a good father? I must be making the right choice, it's for the greater good."_

"No this is much more tactical, that's just going to be plain suicide. We need to attack from all sides, seeing as there will only be at most three of them," Granny explained.

"I agree we must use what they have as weaknesses to our advantage." Charming said.

"How do we know they don't have more people helping them?" Dopey asked.

"We don't," Grumpy replied.

"Well, we have to attack before they get stronger or wreak more havoc. They might've paused for now, but they must be planning something," Red said.

"I'll send a message to Robin and the knights at Regina's castle," David said.

Snow would be very angry if she heard what Charming decided, but would she be able to forgive him?

* * *

Killian and Emma sat across from each other at an enchanted circle table. An image appeared on the round table of David, Grumpy, and others Emma used to call friends. Now, Emma knew what they really wanted, and she couldn't let them have it.

"I guess my father always wanted to keep me from my potential," Emma said.

"Your father never did like me," Killian joked.

The image on the table swirled as Emma waved her hand above it, and then it showed Rumpelstiltskin and Belle.

"The crocodile will always be a coward," Killian sneered.

"Are we going to let him go again? Or are we going to go after him?" Emma asked.

"We should just send Regina out for him."

"Zelena!" Emma called out.

"What? Regina and I were just about to have some fun," Zelena said as she appeared in green smoke with Regina.

"We need Regina to do something love, so will you please give us her heart for a while," Killian said.

"Seriously, I was enjoying myself, but it's not like I have a choice. Here," Zelena said as she handed Killian Regina's heart.

"Thank you," Killian said.

* * *

 **Thanks for reading! Please give me a suggestion on what to do next because I'm having a really bad writers block. If you're enjoying my story so far please leave a review. _lm1212_**


	5. Chapter 5

**Thank you for the suggestion oncerSM, so this flashback will be mostly based off of season 5, but with a better Captain Swan ending if you know what I mean.**

* * *

Flashback

"We went to Camelot for you, how did we disappoint you, and what do you mean this is all for me?" Killian asked as he threatened to throw the squid ink at Emma.

"I'm doing this for us, I'm getting rid of the darkness. Why can't you be happy? Isn't this what you wanted?" Emma replied.

"I want the darkness out of you, but you can't kill Zelena to get rid of it."

"This is the only way."

"No, there has to be another way. We went to Camelot to find Merlin, where is he? He has to be able to help you."

"He can't help us."

"Why can't you just tell me what happened in Camelot? Emma, please give me back my memories." Killian yearned.

"I can't, I'll lose you if I do."

"I will always love you Emma, no matter what."

"I turned you into what you never wanted to be, and you loved it. Killian, we did horrible things together, and I didn't want you to hate me for it."

"You're not making any sense. What can't you tell me?"

"You're a dark one," Emma said, and then Killian's name appeared on Excalibur.

"What? No, that isn't possible, there can't be two dark ones."

"You want your memories Killian? Here," Emma said as a dream catcher appeared in her hand. Memories started flashing in the dream catcher, and slowly Killian's face turned into a dark grin. He remembered the way Emma and him crushed Merlin's heart. He felt Excalibur's cut like it was yesterday, and he remembered feeling the blade cut his skin. He saw the way he begged at Emma not to turn him into a dark one, but she field of pink roses, Merida's heart in Emma's hand, choosing the home he stood in for Emma.

Killian wanted to cry, but the darkness told him not to show weakness. He was powerful, and Emma didn't tell him. They could've had fun and been like they were in Camelot. He had no regret of killing Merlin and by the way Emma looked, she didn't either. They burned a village down together, they tortured Merida together, and they planned for their future in Storybrooke together.

"You could've told me love. Just because I'm a dark one wouldn't mean I would stop loving you. Now I can do what I was never able to do," Killian said honestly.

"What's that?"

"Get my revenge."

"Do you have it?" Emma said.

"Yes love, of course I have it." Hook said as he appeared in red smoke. In his hand was the wizards boney wand.

"Good, now we can get rid of this town. We can live together in a castle in the Enchanted Forest and rule it, and you can get your revenge."

"Let's start."

* * *

Grey and red smoke enveloped the little town Storybrooke. Nobody knew what it was, what it meant, or what was coming. All Regina knew was that it was dark magic, and it had to be Emma. Regina quickly teleported herself to Emma's house, "Emma!" Regina yelled.

"Come in," Emma said and the door magically swung open.

"Emma, what are you doin-" Regina started.

"Killian. What are you doing here?" Regina ended.

"Why don't you just have your memories back instead?" Killian said making a dream catcher appear in red smoke.

"M-magic," Regina started, but then she was flooded with memories. She finally knew what Killian was doing here with Emma, he was a dark one also. He was turned into a dark one by Emma.

"No, what are you doing? What have you done? You enacted something, but I'll do whatever I can to stop it," Regina said.

"Love, this town is going to be destroyed, and then we'll all be in the enchanted forest." Killian said.

"You, you want your revenge on Rumpelstiltskin don't you? I may not be able to stop this curse, but I can make sure you won't know where he is when we get sent to the enchanted forest," Regina stated defiantly.

Regina quickly casted a spell to make sure when everybody reached Storybrooke Emma and Killian would temporarily not be able to move or do anything for an hour. Everything was covered, Regina was knocked out. She woke up again and found herself in the Enchanted forest standing next to all the people of Storybrooke. Regina quickly warned everyone what happened, and they all fled. Only Killian and Emma were left, and the couldn't do anything. Time moved by, but it didn't feel like anything for Killian and Emma, time was now irreverent to them. Finally, an hour passed and Killian yelled, "The damn evil queen. She's going to regret what she did."

Emma held Killian back and said, "Don't forget what we came here to do, why we sent everybody back to here. Let's find ourselves a home, and then we can start.

* * *

 **Thank you for the positive reviews, please keep leaving them. They really help me want to write more chapters. Thank you for reading I hope guys enjoyed. _lm1212_**


	6. Chapter 6

"Sir Henry, we'll reach the castle in a few hours," A knight said.

"Thank you, Stephen," Henry replied.

"We should all rest. We've been journeying for hours, and the horses need a break," Robin said.

"No, once I find mom then we can rest, but there isn't rest until we find her," Henry said.

"But sire," Stephen started.

"No," Henry stated.

"Henry, the horses need a break. You need a break," Robin said.

"Fine, but only for thirty minutes, then we continue," Henry said.

"Men, set up camp. Thirty minutes only!" Stephen yelled.

Everybody immediately got off their horses and pulled off the supplies from their horses and started setting up tents. It was a hot day and all the men were eager to have a break from the sun above them. Henry frustratingly hopped off his horse and set down his stuff for camp.

* * *

Regina appeared in purple smoke. She tried resisting the order of the dark one, but it didn't work. She ended up at Rumpelstiltskin's home, and lo and behold, Rumpelstiltskin and Belle were there. Rumpel scurried about as he and Belle quickly stuff clothes and items into their bags, and Rumpelstiltskin looked up to see Regina and said, "Regina? What are you doing here?"

"I'm sorry Rumpel," Regina started. She raised her hand in the air and put Rumpel and Belle to sleep.

* * *

"Why is Gina taking so long?" Zelena complained.

"Will you stop complaining, Zelena?" Emma said.

Regina suddenly appeared and so did Rumpelstiltskin and Belle. Rumpelstiltskin and Belle laid on the ground unconscious. "I need to see Henry. Emma, please let me go," Regina said.

"No, love," Killian said as he held Regina's heart. He tossed it to Zelena and said, "Here's the heart back. Don't get in our way Zelena."

* * *

 **Thanks for reading! Sorry for the really short chapter, but I hope you enjoyed. _lm1212_**


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